Primary Citation PubMed: 18227510
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Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.
(2009) PLoS Comput Biol 5
PubMed: 19714203 | PubMedCentral: PMC2722018 | DOI: 10.1371/journal.pcbi.1000487
(B) Superposition of the predicted structural cluster between EGFR-T790M and DFG (in blue) with the crystallographic conformation (pdb entry 2JIT, in green) (C) Similarity in the predicted structure a... d packing interactions between the DFG conformation and the gatekeeper residues T315I in ABL (dark blue) and T790M in EGFR (light blue).
(B) Superposition of the predicted structural model of the EGFR-T790M mutant (in blue) with the crystal structure of EGFR-T790M (active form, pdb entry 2JIT, in green).
Publication Year: 2009
Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases.
(2011) PLoS Comput Biol 7
PubMed: 21998569 | PubMedCentral: PMC3188506 | DOI: 10.1371/journal.pcbi.1002179
Allosteric Signatures of Mutation-Induced EGFR Activation In this section, we analyzed allosteric signatures of the EGFR kinase catalytic domain using the results of MD simulations in the following fu... ctional states: the inactive EGFR form (PDB ID 1XKK)  ; the active EGFR form (PDB ID 2J6M)  , the active form of the EGFR-T790M mutant (PDB ID 2JIT)  .
Structural mapping of residues involved in long-range communication in different functional states of the EGFR catalytic domain: ( A ) the inactive EGFR-WT structure (PDB ID 1XKK); ( B ) the active EGFR-WT structure (PDB ID 2J6M); ( C ) the active form of the EGFR-T790M mutant (PDB ID 2JIT).
In MD simulations of the ABL and EGFR kinase domains, we used the following crystal structures : PDB ID 1IEP (inactive ABL structure)  , PDB ID 1M52 (active ABL structure)  ,  , PDB ID 2G1T (Src-like inactive ABL structure)  , PDB ID 2Z60 (the active form of the ABL-T315I mutant)  , PDB ID 1XKK (Src/Cdk-like inactive EGFR structure)  , PDB ID 2GS7 (Src/Cdk-like inactive EGFR structure)  , and PDB ID 2J6M (active EGFR structure)  , and PDB ID 2JIT (EGFR-T790M mutant)  .
Publication Year: 2011
Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.
(2014) PLoS One 9
PubMed: 25427151 | PubMedCentral: PMC4245119 | DOI: 10.1371/journal.pone.0113488
The computed B-factors describe time-averaged fluctuations of heavy atoms obtained from simulations of (A) Cdk/Src-IF1 EGFR-WT (pdb id 1XKK, in blue), (B) Cdk/Src-IF2 EGFR-WT (pdb id 2RF9, in red), (C... active EGFR-WT (pdb id 2ITX, in green), (D) active EGFR-L858R (pdb id 2ITV, in red), (E) active EGFR-T790M (pdb id 2JIT, in green), (F) inactive EGFR-L858R (pdb id 4I20, in red), (G) inactive EGFR-L858R/T790M (pdb id 4I21, in green), (H) inactive ErbB4-WT (pdb id 3BBT, in green), (I) active ErbB4-WT (pdb id 3BCE, in maroon).
(B) The computed B-factors obtained from simulations of the active structures of EGFR-WT (pdb id 2ITX, in blue), EGFR-L858R (pdb id 2ITV, in red), and EGFR-T790M (pdb id 2JIT, in green).
Structural similarities in the functional regions of the active EGFR-WT conformation (in blue), DFG-in/αC-helix-in (pdb id 2ITX, 2J6M); the active EGFR-L858R conformation (in red), DFG-in/αC-helix-in (pdb id 2ITV); and the active EGFR-T790M conformation (in green), DFG-in/αC-helix-in (pdb id 2JIT).
The active EGFR crystal structures used in simulations included the following pdb entries: pdb id 2GS2 (active, Apo EGFR-WT); pdb id 2ITX (active, EGFR-WT in complex with AMP-PNP); pdb id 2J6M (active, EGFR-WT in complex with AEE788 inhibitor); pdb id 2ITV (active, EGFR-WT in complex with AMP-PNP); and pdb id 2JIT (active, Apo EGFR-T790M).
Publication Year: 2014
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